Genome and Proteome Analysis of Rhodococcus erythropolis MI2: Elucidation of the 4,4´-Dithiodibutyric Acid Catabolism

Abstract

Rhodococcus erythropolis MI2 has the extraordinary ability to utilize the xenobiotic 4,4´-dithiodibutyric acid (DTDB). Cleavage of DTDB by the disulfide-reductase Nox, which is the only verified enzyme involved in DTDB-degradation, raised 4-mercaptobutyric acid (4MB). 4MB could act as building block of a novel polythioester with unknown properties. To completely unravel the catabolism of DTDB, the genome of R. erythropolis MI2 was sequenced, and subsequently the proteome was analyzed. The draft genome sequence consists of approximately 7.2 Mbp with an overall G+C content of 62.25% and 6,859 predicted protein-encoding genes. The genome of strain MI2 is composed of three replicons: one chromosome and two megaplasmids with sizes of 6.45, 0.4 and 0.35 Mbp, respectively. When cells of strain MI2 were cultivated with DTDB as sole carbon source and compared to cells grown with succinate, several interesting proteins with significantly higher expression levels were identified using 2D-PAGE and MALDI-TOF mass spectrometry. A putative luciferase-like monooxygenase-class F420-dependent oxidoreductase (RERY_05640), which is encoded by one of the 126 monooxygenase-encoding genes of the MI2-genome, showed a 3-fold increased expression level. This monooxygenase could oxidize the intermediate 4MB into 4-oxo-4-sulfanylbutyric acid. Next, a desulfurization step, which forms succinic acid and volatile hydrogen sulfide, is proposed. One gene coding for a putative desulfhydrase (RERY_06500) was identified in the genome of strain MI2. However, the gene product was not recognized in the proteome analyses. But, a significant expression level with a ratio of up to 7.3 was determined for a putative sulfide:quinone oxidoreductase (RERY_02710), which could also be involved in the abstraction of the sulfur group. As response to the toxicity of the intermediates, several stress response proteins were strongly expressed, including a superoxide dismutase (RERY_05600) and an osmotically induced protein (RERY_02670). Accordingly, novel insights in the catabolic pathway of DTDB were gained.

Biodesulfurization Induces Reprogramming of Sulfur Metabolism in Rhodococcus qingshengii IGTS8: Proteomics and Untargeted Metabolomics

“…Although stimulation of the oxidative stress response in the dibenzothiophene culture, evident from the upregulation of alkylhydroperoxide reductase, agrees with previous studies ( 22 , 60 ), the upshift in biosynthesis of the low-molecular weight thiols mycothiol and ergothioneine under biodesulfurization conditions has not been reported to date. Accordingly, we propose to extend the list of the sulfur starvation-induced proteins to include enzymes of low-molecular weight thiols biosynthesis.…”

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

“…), R. erythropolis exhibits an increased resistance to the concomitant strong oxidative stress arising from the toxic substrate decomposition and leading to the accumulation of highly reactive oxygen species, H 2 O 2 , and highly toxic lipid peroxides. Additionally, the induced activity of antioxidant enzymes due to the overexpression of antioxidant-encoding genes (cytochrome P450, catalase, superoxide dismutase, alkyl hydroperoxide reductase, and the protective protein RecA) involved in DNA repair, detoxification of reactive oxygen species, and, finally, in detoxification of pollutants, has been observed [ 99 , 100 ]. Morphological changes occur, particularly changes in size and shape, in addition to an increase in the number of cytoplasmic polyphosphate inclusions (volutin), hypertrophy of individual organelles, and the formation of multicellular aggregates, biofilms, and other spatial structures.…”

Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency

“…All the previous proteomic investigations, which were performed on Rhodococcus , only highlighted its catabolic behavior towards different organic compounds viz . Fluoranthene 14 , toluene and phenol 15 , propane 16 , triacylglycerol 17 , 4,4′-Dithiodibutyric Acid 18 , benzoate 19 and polyaromatic compounds 20 . In this perspective, the present study for the first time unravels its proteomic response towards the abiotic stress and identified a protein biomarker for low-temperature nitrogen deficient conditions.…”